[BioC] read.maimages

Gordon Smyth smyth at wehi.edu.au
Wed Feb 4 00:38:55 MET 2004

At 10:04 PM 3/02/2004, Jason Skelton wrote:
>I'm guessing the answer to my question is YES but are the Rb and Gb parts 
>of read.maimages still compulsory ?
>Or can I some how ignore them ?

Short answer is yes. But you can work around this by reading arbitrary 
columns into Rb and Gb and then nulling them:

RG <- read.maimages(files, 
RG <- backgroundCorrect(RG, method="none")


>I'm using some software (BlueFuse) that isn't supported by limma so I need 
>to specify the column headers but the software
>doesn't give background values just values for Cy3 & Cy5 as it's approach 
>is different to other spot finding programs.
>So at the moment I'm having to make new columns for the background and 
>give them values of 0 for each gene.
>I've searched the mail achives and could only find this message from June 
>2003 I was asking just in case anything has changed since then OR is there 
>an option for making Rb & Gb NULL
>or FALSE or something similar
>Message: 4
>Date: Thu, 19 Jun 2003 10:09:13 +1000
>From: Gordon Smyth <smyth at wehi.edu.au>
>Subject: Re: [BioC] read.maimages
>The limma help documentation for 'read.maimages' says:
>    columns: list with fields `Rf', `Gf', `Rb' and `Gb' giving the column
>           names to be used for red and green foreground and background.
>So you need something like
>   columns=list(Rf="Cy5",Gf="Cy3",Rb="Cy5.background",Gb="Cy3.background")
>The names in double quotes are the column names in your file. The rest of 
>the syntax is compulsory!
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute
>CB10 1SA
>Tel +44(0)1223 834244 Ext 7123
>Fax +44(0)1223 494919

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